Computational Chemistry Lab(1)

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Name: ___________________________
Chemistry
Period: ________
Date: _______
Computational Chemistry Lab
“Start-of-Class Question”:
1. Draw the Lewis Diagram for the molecule HCOOH (The C is bonded to 2 “O”s and 1
“H”.) What is the molecular geometry around the Carbon? What is the molecular
geometry around the central Oxygen?
Part A: Molecular Geometry
1. On a computer log in to: molview.org
2. Hit the trash can button to clear the default molecule. You can build your own molecules
on the left side and then click ​2D → 3D ​to see the 3-dimensional structure on the left.
Scroll in and out using the mouse to zoom in/out on your molecules.
3. Click the C and place a Carbon atom on the left side of the screen in the “build space.”
4. Click the F and add 4 Fluorine atoms bonded to the Carbon atom that you already have.
To create a bond: start by clicking on the Carbon and dragging the Fluorine to
where you want it on the screen. (Yes, the C might disappear - it is actually still
there but sometimes in structures we leave out “C”s as a shorthand way to write
things.
5. Click ​broom ​button to “clean” the molecule, minimizing the energy. This puts the
molecule in the correct geometry.
6. Click ​2D → 3D ​and examine the 3D structure that’s created. Describe the molecular
geometry (linear, trigonal planar, bent, trigonal pyramidal, tetrahedral) and record your
answer Date Table #1.
7. Under the Jmol tab, select ​Distance. ​Click on two atoms to measure the distance in
nanometers between them - this is the bond length.
8. Measure all the different bond lengths in the molecule and record your values in Data
Table #1.
9. Under the Jmol table, select ​Clean. T
​ his clears all the lines that you just drew.
10. Under the Jmol tab, select ​Angle. ​Click on one atom, click on a second atom, and the
double click on a third atom to measure the bond angle between them.
11. Measure all the different bond angles in the molecule and record your values in Data
Table #1.
12. Hit the Trashcan to delete the molecule and then build the other molecules listed in Data
Table #1 and record the information for each of them following steps 5 - 12.
13. Answer analysis questions #1-4
DATA TABLE #1:
Molecule
Geometry
Bond Lengths
Bond Angles
CF​4
PH​3
H​2​O
C​2​H​6
C​2​H​4
C​2​H​2
NaCl
Part B: Polarities
14. Clear any molecules that you currently have in molview.
15. Build CH​3​Cl.
16. Click ​broom b
​ utton to “clean” the molecule, minimizing the energy. This puts the
molecule in the correct geometry.
17. Under the Jmol tab click ​Bond Dipoles.​ This places arrows on the bonds to show you
what the direction electrons are pulled in if the bond is polar. In the Bond Polarity box in
Data Table #2 record which bonds are polar and the direction of electron pull.
18. Clean the structure under Jmol. And select Overall Dipole. This gives you an overall
direction of electron pull in the structure (aka molecular polarity). If no arrow is present
then that means there is either no electron pull OR the electron pull is in opposite
directions and therefore the molecule has a net pull of ZERO. Record this information in
the box in Date Table 2.
19. Under the Jmol tab select ​MEP Surface. Y
​ ou two options, opaque and lucent, chose
whichever one you like better. This shows you the electron cloud around the molecule
and the amount of electron density around the atoms. Record information about this
cloud in Data Table 2 (red is negative, blue is positive, yellow is neutral, and describing
whether it is symmetrical or asymmetrical.
20. Repeat Steps 14 - 19 for the other compounds in Data Table #2.
21. Answer Analysis Questions #5 - 8.
DATA TABLE #2
Molecule
CH​3​F
CF​4
HCl
NH​3
Bond
Polarities
Molecular
Polarity
Electron Cloud/Electron Densities
C​2​H​6
CO​2
H​2​O
C​2​H​2
CH​3​OH
NaCl
C​2​H​4
Part C: The Benzene Molecule
22. With molview draw the structure for C​6​H​6​. (You might want to draw it on paper first.)
23. Then add one more bond using the bond button on the left menu bar. Use this bond to
connect the last Carbon on the left to the Carbon all the way on the right. Yes this will
look really weird right now.
24. Click 2D → 3D to see this molecule 3 dimensionally.
25. Find the geometry around each Carbon atom, each bond length, and each bond angle.
Record all this in Data Table #3.
26. Answer Analysis Question #9 - 11
27. Using molview create your own molecule. They can be as crazy and huge as you want.
The crazier the better. Create a 3D representation and then answer question #12
DATA TABLE #3
Molecule
Geometry
Bond Lengths
Bond Angles
C​6​H​6​ (Benzene)
Analysis Questions:
1. What do you notice about the number of unbonded electron pairs on the central atom
and the bond angles in a molecule?
2. Thinking about repulsion and attraction of particles, which do you think causes more
repulsion, unbonded electron pairs or bonds? What does this do to bond angles?
3. Which bonds tend to be longer (double bonds, single bonds, or triple bonds)? Which
bonds tend to be shorter? Compare the molecule C​2​H​6 to
the molecule C​2​H​2​ and C​2​H​4​ to
​
figure this out.
4. How does the molecular symmetry affect the overall dipole of the molecule?
5. How do the bond dipoles affect the overall dipole of the molecule?
6. What do you think the term “dipole” actually means?
7. How can the MEP Surface view be used to describe the electron density around a
molecule?
8. During the first part of lab you investigated which kinds of bonds were longer/shorter. Do
the bond lengths for benzene (C​6​H​6​) correspond to what you thought they should be?
9. Watch the video that on the Google Classroom assignment, then describe what
resonance means and it means if a structure has multiple resonance forms?
10. After watching the video, why do you think the bond lengths on benzene were different
from what you expected?
11. Investigate the molecular geometry around each of the central atoms in your benzene
molecule as well as the bond polarity and molecular polarity for benzene.